Unfinished Business
by SGAFan
Summary: He'd nearly killed her. Sure, John hadn't exactly been in control of himself, but can he accept that reason? Conversion missing scene story.


_**Unfinished Business**_

He woke.

John stared at the ceiling for a moment, as the darkness of his corner of the infirmary gradually came into focus. Ironically, he was relieved to wait the precious few seconds it took for his eyes to adjust…the last time it was dark, he still saw with inhuman clarity. John slowly lifted his hand, relieved this time, to be free of the restraints. He was no longer dangerous…unpredictable…untrustworthy. He stared at the fading scales lining his knuckles and fingers. Once again, he was John Sheppard and he was human.

John inhaled deeply and closed his eyes, his mind wandering. The past week was confusing to him at best. With only snatches to go on, John couldn't fill in the holes in his memory…and part of him didn't want to. Faint images of running through Atlantis, attacking his own men, falling to Ronon's stunner, flashed through his mind. Climbing walls, smashing Elizabeth's window, kissing Teyla…John opened his eyes and grimaced. Kiss hell, attack was more like it. He owed her a big apology for that one.

Like some jigsaw puzzle, pieces of his memory slowly formed the picture of his life from the last few days…and John didn't like what he was seeing. More than what he'd done, it was the memories of his road to insanity that troubled him the most. He'd felt it. Overpowering instinct…destruction…hate had crept into him. John was slowly remembering that the whole time he'd known what was happening…and couldn't stop it. It was like an anger he couldn't control…couldn't master. Strengthened by the virus inhibitors, John had been painfully aware as the retrovirus had eaten away at his rational mind. Vague images of Elizabeth flashed through his memory. He'd known then. Known that he was losing his fight against the virus, known that one guard on his door wasn't enough…known that he was dangerous. The look he'd seen in her face told him she'd known it too. She'd grown scared of him and she had every reason…

John's eyes snapped open as new and painful memories washed over him. He saw the fear in her eyes, felt her fragile neck in his grip…knew how close he'd come to crushing it.

John pulled in a ragged breath and clenched his teeth as he squeezed his eyes shut against the image…the feelings, but they still plagued him. Not much of John Sheppard had been left by then, but what was there, had stopped him from killing her…only barely. The fear in her eyes, the weak grip of her hands on him, her cough…her gasps, all of it assaulted him, as this new and unwelcome memory flooded over him. He felt himself let her go, heard her fall heavily to the floor…

John opened his eyes and sat up in bed. "Elizabeth," he whispered. He swallowed hard and pursed his lips, as his mind tried to process all this new information. She'd been there, every day, sometimes more than once, to see him. As lucidity had gradually returned to him, never once did John ever feel tension from her. A very faint smile pulled at his mouth. She didn't blame him, but guilt shadowed him anyway. Relieved to be off the IV and onto routine injections, John realized he had unfinished business with Elizabeth, and now was as good a time as any to finish it.

He looked up, motion from the other side of the privacy barrier grabbing his attention. John smiled and nodded at Lansing, one of Beckett's medics. He swung his legs off the bed, an action that immediately brought Lansing to his side.

"Colonel, do you need something?"

John looked around. "My clothes would be a good start." He flashed a charming smile at Lansing, who blushed slightly.

"I'll see what I can do." She turned and walked away, leaving John alone. He looked around before slowly standing. At first, his legs felt weak, but as he eased more weight onto them, John could feel the unsteadiness wearing off. He looked down at his legs and smiled at the perfectly human frailty.

"What do ye think you're doing?"

John's gaze shifted up and into the uncompromising glare of Carson Beckett. "Doc." Seeing no sign of the pretty medic, John frowned. "Lansing?"

"Aye, she told me you were out of bed," Carson arched an eyebrow, "and that you tried to charm your clothes out of her. I'll ask ye again. What do ye think you're doing?"

"Busted." John leaned back against his bed and sighed. "Look, Doc, I need to talk to Elizabeth. It's important."

"She'll come by tomorrow tell her then." Carson pushed gently but insistently on John's chest, trying to get him to lay down, but John wouldn't relent.

"It can't wait. I need to talk to her now. Come on, Doc, I could use the walk anyway. My legs are stiff from lying in that bed. Just up to her office and straight back. I promise." John arched his brows imploringly at Beckett.

Carson sighed and stared a long moment at the Colonel. "Alright. If ye feel spry enough, the walk would do you good. But," Carson pointed emphatically at John, "there and straight back. No arguments."

John smiled. "Thanks, Doc."

Carson grunted quietly as he disappeared around the privacy barrier.

Watching Beckett go, John felt a strange knot in his gut and it took a moment for him to realize it was nerves. _What the hell are you nervous about? _John chastised himself. In all of her visits, Elizabeth hadn't shown one sign of anger or fear...only the steadfast friendship she and he had come to share since this whole adventure had begun.

John smiled slightly as Beckett reappeared, John's clothes in hand.

"To Weir's office and back." Carson reiterated strongly. "Any other field trips and I'll have security by your bed for the next two weeks." Beckett arched an uncompromising brow at Sheppard.

"Two weeks?" John questioned, "you told me this afternoon I'd only be here for another week at the most."

An almost wicked smile crossed Beckett's face. "Aye."

John stiffened in surprise at the downright cunning angle Beckett was using on him. Sheppard arched his brows. "Ah. Right. Weir's office and straight back." John's gaze narrowed. "You're enjoying this too much, Doc."

Carson smiled broadly. "Aye." He turned and left, leaving a chuckling Sheppard some privacy to dress.

John slowly pulled his pants and shirt on, deliberately extending the occasional supporting hand to the edge of his bed as weakness in his legs came and went. Normally, the weakness would bother him, but today, he relished it. Unnatural and abnormal, the strength from his conversion had, at a deep level, scared the hell out of him. It had been one more part of himself he'd lost control of, and now, to weakly stand next to his bed, John felt a strange satisfaction.

He sat in a chair next to his bed and quickly laced his boots, before slowly standing. His right leg felt naked, as he keenly felt the absence of his side arm, but John paid it no heed. Slowly, he walked out from his private corner of the infirmary, and headed for the door.

Momentarily catching Carson's glance, John nodded slightly in gratitude.

Carson smiled back, his understanding smile tinged slightly with a challenging look. "Don't be long, Colonel," Carson added.

John nodded before exiting the infirmary. Pausing in the hallway, he looked around. The normally busy hallway was quiet at the late evening hour, and briefly John wondered where Elizabeth would be. He almost immediately dismissed the question. Weir was one of the most driven and dedicated people he'd ever met and John was willing to lay odds she was still in her office.

Heading for the control deck, John passed a few scattered personnel on his way, some of them nodding in recognition to him, gestures he returned. As he came to the transporter, which would carry him up to the command deck, John paused. A wry smile crossed his face as he turned and elected the stairs instead. The more he walked, the better he felt. Mostly, it was just getting out of the infirmary, but his long inactive muscles relished the activity and John was determined to make the most of the chance he had.

He ascended the first flight, and paused on the mid level landing. Slightly winded, and feeling fatigue in his legs, John was mildly irritated at the lingering weakness in his body, but forced perspective to himself. It was a sign of recovery...humanity, and he'd be damned if he was going to be irritated over that. After taking a minute, he continued on his way, his ascension of the last flight of stairs leaving him only mildly winded.

"Colonel? Huh, does Beckett know you're here?" Rodney McKay's head popped up from behind one of the Ancient consoles.

John arched an eyebrow at McKay's question. "Nice to see you too, Rodney," he quipped, "as a matter of fact, yes."

McKay fidgeted slightly. "Oh, well, it's good to see you up and about."

John smiled slightly at McKay's predictably uncomfortable expression. Niceties were never his strong point anyway. "Thanks." Giving a slight nod to McKay, John continued across the control deck and towards Weir's office.

Still a dozen feet away, John paused, his eyes settling on Elizabeth. The large window he'd smashed had since been replaced, but the memory stopped John in is tracks. The evil...the darkness within him had already started to affect him that day. At some level he'd been desperate. Wanting...needing to do **something** to help his team help him. Looking back, there was no question that he wasn't fit to go off world, but at that moment, he'd been so sure, so driven that nothing else had mattered. John lifted his right hand and looked down at the fading dark scales crossing his knuckles. He hadn't even felt it. He didn't even know his own strength, but his rash reaction had left him stunned. John swallowed. Just one item on a long list of things he needed to apologize for.

He pulled in a deep breath and walked the rest of the way to Weir's office. In the doorway he paused, watching as she went about her work, unnoticing of his presence. Determined not to delay the inevitable, John quietly cleared his throat.

Elizabeth looked up a smile immediately coming to her face. "John. It's good to see you out of bed." She waved him forward. "Come in."

"Thanks." John's reply was quiet, and he immediately fell into a silence following it. He slowly walked into her office and stood behind one of the chairs opposite her desk. Standing there, John's mind raced as he tried to think of what to say.

Elizabeth's gaze narrowed at his silence. "John? Are you okay?"

John sighed deeply. "Elizabeth, I..." He looked away. He didn't know what to say. What could he say? I'm sorry for grabbing you by the throat and throwing you against a wall? I'm sorry for scaring the hell out of you? For hurting you? For nearly killing you? Movement by Weir caught his eye and John looked up, watching as Elizabeth stood and rounded her desk.

"John? What's wrong?"

Her tone was caring and concerned, and that concern only reaffirmed in John's mind why he was standing there in the first place. "Why didn't you tell me?" He blurted out.

Weir looked at him in confusion for a moment, before realization dawned on her. She pursed her lips. "I didn't think it was necessary."

"I nearly killed you and you didn't think it was necessary?" John's tone was incredulous as he stared at her in open shock. "I could've killed you," he reiterated, "I...I almost did."

"No." Elizabeth contradicted him firmly. "It wasn't you, John."

John was unconvinced. "Elizabeth…" His voice trailed off as Weir interrupted him.

"No, John, listen to me," she walked closer to him, her serious gaze imploring. "You can't hold yourself responsible for what happened."

John cocked his head. "Can't I?" He stared intently at her. "It was me. It was my hand on your throat." John's breathing quickened slightly. "You don't know how close I came to…" His voice trailed off. John inhaled deeply. "I saw the fear in your eyes, Elizabeth." He held her gaze as Weir slowly nodded. She walked a few steps away from him, only to turn back and face him.

"I won't lie to you. I was terrified. Not of you, but of that…thing. That creature you were trapped inside of." She sighed and shook her head before walking back to him. "But, I'm still here. You didn't let that thing kill me, John, think about that."

John ran a hand through his hair and turned away. "There wasn't much of me left by then. I knew…I felt what was happening, but I couldn't stop it."

"You don't have to tell me this, John," Elizabeth interrupted quietly.

Sheppard looked at her. "Yes, I do. I owe you that much."

Elizabeth nodded silently and eased over to her office door, which she slowly pulled shut. "Okay."

John stared out the window at the darkened gate room and inactive Stargate. "I was loosing myself, Elizabeth, and I knew it. It's…hard to explain, I don't even really understand myself, but I wanted to find a way to be me again." John's brows wrinkled in confusion. "It was like everything I wanted, needed, were twisted by that damn virus. Twisted into something…evil." He turned and stared evenly at her. "I wanted you to help me," John bit off every word of the difficult admission, but went on, "and," he waved his had briefly, "that happened."

"We tried," Elizabeth answered quietly. "I would've done almost anything to help you, John…except get more people killed."

"I know and you were right." Frustration passed through his expression. "Two men died trying to save me."

"John," Elizabeth sighed, "what are you trying to tell me?"

A cynical half smile passed over John's face at her direct question. "I don't know," he admitted, "except that I'm sorry. More sorry than you know."

Elizabeth crossed her hands in front of her and walked across her office to him. "Hey," she said quietly, grabbing his attention. "You have nothing to be sorry for."

"I don't…" John's voice trailed off as Elizabeth interrupted him with a raised hand.

"Hear me out."

John sighed and nodded.

"If the retrovirus would've taken over completely, would you have killed me?"

John pursed his lips and looked away for a moment, before once again meeting her even stare. "Yes," he replied quietly.

Unsurprised, Weir nodded. "Then I'm alive because you," she pointed at him, "John Sheppard didn't let that happen. You saved my life, Colonel, I should be thanking you."

John's gaze narrowed intently. "It's not that simple." He arched his brows slightly at her smile.

"Yes, it is."

John turned away and once again stared at the gate, Weir's words sticking with him. Respect welled within him, and in the year and a half they had led Atlantis together, John had become all too familiar with it. The deep sense of respect she'd kindled within him only grew…and in a moment of clarity, John realized it was that respect that had saved her…and him.

His mind played over that dark moment in his quarters, and John forced himself to look at it. In a moment of clarity he'd felt her throat in his grasp, seen her fear…and sensed the wrongness of it all. John Sheppard was nearly gone, but what was left had surged forward, momentarily smothering the darkness. He knew the value he placed in her friendship…and the value she placed in his. He knew she would've done almost anything to help him, and saying no was something she had to do, not what she wanted to do. He admired her courage, and her strength to do the right thing, no matter how hard it was or how much she wanted something else. It was that admiration, that respect, that ultimately saved her life.

At that moment, from deep inside him, John, at some level, still existed, still felt that respect, and fought to save the recipient of it. For if he'd killed her, John knew what was left of John Sheppard would've died with her.

"John?"

He turned, meeting her questioning gaze with a relaxed one of his own. "You're welcome," he said quietly, a small smile flashing across his face as her expression softened.

"Can we put this behind us now, Colonel, and get on with business?" Weir arched an eyebrow at him.

Her words once again kindled that respect within John as he nodded slowly. "Yeah, I think we can." His gaze narrowed as Elizabeth's hand touched her headset in response to a hail.

"This is Weir." Her eyes flashed to John for a moment, before she smiled in genuine amusement. "Yes, Carson, he's here." She paused, nodding as her smile broadened. "Will do. Weir out." Elizabeth stifled a giggle and looked at John.

"What?" John arched a suspicious brow.

"That was Dr. Beckett. He's looking for you. Apparently, you were not supposed to be gone long. He said something about a guard on your bed for two weeks?"

John grimaced. "I've only been gone for fifteen minutes," he muttered. He flashed Weir a mock serious stare as she giggled quietly.

"You better get going then. He said, and I quote, 'The Colonel has exactly five minutes to get back in my infirmary or he'll will have a guard on his bed for the next two weeks.'"

"Right." John sighed. He opened the door and paused, before looking back and making eye contact with Weir. Something, he felt, wanted to be said, but as he stood there, for the life of him, John couldn't think of what. Finally, he just nodded once at her, smiling slightly as she did the same to him.

"Get some rest, Colonel." Weir smiled.

John nodded, feeling a smile come to his face as well. "Will do." Feeling as though a burden had been lifted, John turned and left._  
_

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_Author's notes:_

_John mentioned in the end of Conversion that things were slowly coming back to him. I wondered what he thought the moment he remembered that he attacked Weir and could've killed her. At the very least he scared the heck out of her. I can't imagine that John would've just let that go…but at the same time, I don't see Weir wanting to make a big deal of it. _

_I thought that would be something interesting to explore. Hope you liked my interpretation!_

_SGAFan_


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